PXCONTRATES(1)

📦
version 1.3.2 · 3 versions
, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 PXCONTRATES 💖

okay bestie, so pxcontrates is a user command from the phyx fam (version 1.3.1) and it does continuous character rate estimation with Brownian and OU. that's the whole vibe. she's giving phylogenetics main character energy and she's literally so good at it 🧚✨

✨ SYNOPSIS ✨

pxcontrates [OPTIONS]...

🌸 DESCRIPTION 🌸

so like, continuous character rate estimation with Brownian and OU — that's her thing, that's her moment, no cap. 🦋

and the way she eats file formats?? she will take fasta, phylip, and nexus formats from a file or from STDIN. flexible queen 💅

🎀 OPTIONS 🎀

  • -c, --charf=FILE — input character file. if you don't give her one she'll just read from STDIN instead, nbd 🫶
  • -t, --treef=FILE — input tree file. again, STDIN otherwise. she's not picky 💖
  • -a, --analysis=NUM — analysis type. your choices are 0=anc (which is the DEFAULT, periodt) or 1=ratetest. pick your fighter ⭐
  • -o, --outf=FILE — output sequence file. if you skip it you get STOUT otherwise 👑
  • -h, --help — display this help and exit. classic, iconic, we love her 💀
  • -V, --version — display version and exit. just the numbers, no small talk 🌈
  • -C, --citation — display phyx citation and exit. cite your sources bestie, it's giving academic integrity 🎓✨

📚 CITATION 📚

if you use this (and you should, she ate), cite the girlies:

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

lowkey legendary paper fr fr 💜

✍️ AUTHOR ✍️

Written by Stephen A. Smith (blackrim). ty for your service king 🫡💖

🐛 REPORTING BUGS 🐛

found a bug? not me manifesting one, but if you did, report it here:

they wanna hear from you, bestie 🙈

Copyright © 2013-2024 FePhyFoFum License GPLv3 💅

so yeah, that's the whole page — pxcontrates version 1.3.1, dated June 2024. go forth and estimate those rates, my little phylogenetic fairy 🧚🌸💖

📦 where this page comes from